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Language Skills

R
Bash
Python
AWK
SQL
Perl

Disclaimer

Made with the R package pagedown.

Based on the Nick Strayer’s CV package; modified source code for this CV is available here.

Last updated on 2020-02-16.

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Kasia Kedzierska

I am a 2nd year DPhil Candidate at the University of Oxford, studying the chromatin organisation in endometrial cancer. As a bioifnormatician, I spend most of my time either in command line writing Bash/Awk scripts or doing data analysis in R/Python.

I like teaching and deeply believe in Open Science. I am the President of #NGSchool Society with which I’ve been organising Summer Schoools in Bioinformatics. During last year edition - #NGSchool2019: Machine Learning for Biomedicine we recorded and published some of the lectures. This year, during #NGSchool2020: Statistical Learning in Genomics and 5 year anniversary conference we plan to record many more.

Research Experience

DPhil Candidate

Church group @ Wellcome Centre for Human Genetics, Wedge group @ Big Data Institute

University of Oxford, UK

2022 - 2018

  • PhD project: Functional and evolutionary characterisation of chromatin organisation in endometrial cancer

Visiting Graduate Student

Ratan group

University of Virginia, USA

2018 - 2017

  • Developed SONiCS - a tool for genotyping short tandem repeats (STRs) profiled using capture assays.
  • Worked on the Master thesis - Analysis of the mutational burden across gene sets in cancer.

Visiting Graduate Student

Pemberton group

University of Virginia, USA

2017 - 2016

  • Worked on Epigenetic regulation in prostate cancer.
  • Performed experiments and analyzed data from RNA-seq, ATAC-seq, and ChIP-seq assays.

Research Assistant

Zebrafish Developmental Genomics

IIMCB, Warsaw, Poland

2016 - 2015

  • I worked on the project: Elucidating gene regulatory network of zebrafish heart development using genomics.
  • I was responsible for both computational and experimental aspects of the project.

Education

DPhil. Candidate, Genomic Medicine and Statistics

Nuffield Department of Medicine, Brasenose College

University of Oxford, UK

2022 - 2018

  • Functional and evolutionary characterisation of chromatin organisation in endometrial cancer
  • Wellcome Trust Studentship

M. Sc. Eng., Biotechnology

Warsaw University of Technology

Warsaw, Poland

2018 - 2015

  • Thesis: Analysis of the mutational burden across gene sets in cancer.
  • Thesis awarded the title of the best Master thesis in Bioinformatics defended in 2018.

B. Sc. Eng., Biotechnology

Warsaw University of Technology

Warsaw, Poland

2015 - 2011

Publications

Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development

Genome Research

N/A

2019

  • Regulation networks in heart developmnent in zebrafish.

Genomic analysis of DNA repair genes and androgen signaling in prostate cancer

BMC Cancer

N/A

2018

  • DNA repair genes and androgen signalling in prostate cancer cell lines.

SONiCS: PCR stutter noise correction in genome-scale microsatellites

Bioinformatics

N/A

2018

Posters, and Talks

Analysis of the mutational burden across gene sets in cancer

Polish Bioinformatics Society Symposium

Cracow, Poland

2019

  • Invited talk

Differential mutation analysis across gene sets in cancers

The Biology of Genomes 2018

Cold Spring Harbor, NY, USA

2018

  • Poster

Epigenetic regulation of prostate cancer

Visiting Graduate Traineeship Program Grantees Symposium

Charlottesville, VA, USA

2017

  • Talk

Awards and honours

Best Master Thesis in Bioinformatics       

N/A

N/A

2019 - 2018

  • The Best Master Thesis defended in 2018 in Poland.
  • Analysis of the mutational burden across gene sets in  cancer Masther thesis defended at the Warsaw University of Technology; code for the analyses can be accessed github.com/kzkedzierska/cancers

Visiting Graduate Traineeship Program

N/A

N/A

2017 - 2016

  • The Visiting Research Graduate Traineeship Program offered 12-month research traineeships for outstanding, qualified students from the life sciences at selected institutions in the United States.

Grasz o Staz

N/A

N/A

2015

  • “Grasz o Staz” competition is a national, prestigious and highly competitive (1:25 success rate) scholarship program in Poland organized by PwC.

Teaching Experience

Unsupervised learning, Introduction to Python

#NGSchool2019: Machine Learning for Biomedicine

N/A

2019

  • Tutor for the Introduction to Python (3 h workshop) and for the Unsupervised learning (1,5 h lecture).
  • Materials for the Introduction to Python are available on github

Introduction to R

Wellcome Centre for Human Genetics

N/A

2019

  • 8 week course in Introduction to R, Data Manipulation, Data Visualisation and RNA-seq data analysis.
  • Materials available on github/kzkedziersa/r_intro

ATAC-seq workshop

#NGSchool2017: Single-cell Sequencing

N/A

2017

  • Invited speaker
  • Materials for the course can be available on gitub

Attended Workshops, Summer Schools

Machine Learning Summer School

Imperial College London, University College Londn

London, United Kingdom

2019

  • 12-day intensive course on a variety of topics in machine learning.

Grants

Visegrad Grant to organize #NGSchool2019

Visegrad Fund

N/A

2019

  • 23,500 EUR awarded towards organising #NGSchool2019 allowed to keep the cost of attenting the school to the minimum and record the lectures for broader access.

Non profit work

President

NGSchool Society

N/A

2021 - 2018

  • The goal of the Society is to promote and support science, with emphasis on computational biology.
  • President since 2019; Vice President 2018 - 2019

President

Warsaw Society of Biotechnology

N/A

2016 - 2015

  • Symbioza’s aim is to integrate the biotechnology environment in Poland starting from the youngest generations, and promotion and popularization of biotechnology.